Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003941.1 Kokia drynarioides strain JFW-HI SEQ_117023, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1957
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Found at i:705 original size:28 final size:30
Alignment explanation
Indices: 637--742 Score: 105
Period size: 29 Copynumber: 3.6 Consensus size: 30
627 GTTTGAGGCC
* * *
637 AAATTGTAA-TTTTGGATATC-CGGGGATAA
1 AAATGGTAATTTTTGGATAGCTC-GGAATAA
*
666 AAATGGTAA-TTTTGGATA-CTCGAGAGT-A
1 AAATGGTAATTTTTGGATAGCTCG-GAATAA
* *
694 AAATGGTAATTTTTGGAAAGTTCGGAATAA
1 AAATGGTAATTTTTGGATAGCTCGGAATAA
724 AAATGGTAATTTTTGGATA
1 AAATGGTAATTTTTGGATA
743 TTTGAGGGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 12 0.18
29 31 0.48
30 22 0.34
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.35
Consensus pattern (30 bp):
AAATGGTAATTTTTGGATAGCTCGGAATAA
Found at i:724 original size:58 final size:58
Alignment explanation
Indices: 662--774 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 58
652 ATATCCGGGG
662 ATAAAAATGGTAA-TTTTGGATACTCGAGAGT-AAAATGGTAATTTTTGGAAAGTTCGGA
1 ATAAAAATGGTAATTTTTGGATACTCGAGAGTAAAAAT-GTAATTTTT-GAAAGTTCGGA
* * * *
720 ATAAAAATGGTAATTTTTGGATATTTGAGGGTAAAAATGTGATTTTTGAAAGTTC
1 ATAAAAATGGTAATTTTTGGATACTCGAGAGTAAAAATGTAATTTTTGAAAGTTC
775 AGGGGTAACA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 21 0.43
59 23 0.47
60 5 0.10
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (58 bp):
ATAAAAATGGTAATTTTTGGATACTCGAGAGTAAAAATGTAATTTTTGAAAGTTCGGA
Found at i:755 original size:30 final size:29
Alignment explanation
Indices: 590--957 Score: 166
Period size: 30 Copynumber: 12.6 Consensus size: 29
580 AAAGTGTTAT
*
590 TTTTTGGAAATTTGAGGGT-AGAATGGTAA
1 TTTTTGGAAATTTGAGGGTCAAAAT-GTAA
* ** * *
619 -TTTTAGACGTTTGA-GGCCAAATTGTAA
1 TTTTTGGAAATTTGAGGGTCAAAATGTAA
* ** *
646 -TTTTGGATATCCG-GGGATAAAAATGGTAA
1 TTTTTGGAAATTTGAGGG-TCAAAAT-GTAA
* * * *
675 -TTTTGGATACTCGAGAGT-AAAATGGTAA
1 TTTTTGGAAATTTGAGGGTCAAAAT-GTAA
* ** *
703 TTTTTGGAAAGTTCG-GAATAAAAATGGTAA
1 TTTTTGGAAA-TTTGAGGGTCAAAAT-GTAA
* * *
733 TTTTTGGATATTTGAGGGTAAAAATGTGA
1 TTTTTGGAAATTTGAGGGTCAAAATGTAA
* * *
762 TTTTT-GAAAGTTCAGGGGT-AACATGTAA
1 TTTTTGGAAATTTGA-GGGTCAAAATGTAA
* * *
790 TTTTT-TATAAGCTTAAGGGTCAAAATGTAA
1 TTTTTGGA-AA-TTTGAGGGTCAAAATGTAA
* *
820 TTTTTGGAAAGTTCGAGGGTTAAAATGTAA
1 TTTTTGGAAA-TTTGAGGGTCAAAATGTAA
* * *
850 TTTTTGAGAAGTTCGAGGGTCAAAATGTAT
1 TTTTTG-GAAATTTGAGGGTCAAAATGTAA
* * *
880 TTTTTGAGAAGTTTGAGGGTCAAAATGCAT
1 TTTTTG-GAAATTTGAGGGTCAAAATGTAA
* * ** *
910 TTTTTGGAAAGTTCGGGGGTCAAAACATGA
1 TTTTTGGAAA-TTTGAGGGTCAAAATGTAA
940 TTTTTGGACAATTT-AGGG
1 TTTTTGGA-AATTTGAGGG
958 ACCTTCTAGG
Statistics
Matches: 268, Mismatches: 54, Indels: 34
0.75 0.15 0.10
Matches are distributed among these distances:
27 16 0.06
28 47 0.18
29 54 0.20
30 145 0.54
31 6 0.02
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (29 bp):
TTTTTGGAAATTTGAGGGTCAAAATGTAA
Found at i:764 original size:29 final size:29
Alignment explanation
Indices: 723--934 Score: 178
Period size: 30 Copynumber: 7.1 Consensus size: 29
713 GTTCGGAATA
*
723 AAAATGGTAATTTTTGGATA-TTTGAGGGTA
1 AAAAT-GTAATTTTTGGA-AGTTTGAGGGTC
* * *
753 AAAATGTGATTTTTGAAAG-TTCAGGGGT-
1 AAAATGTAATTTTTGGAAGTTTGA-GGGTC
* ** * *
781 AACATGTAATTTTTTATAAGCTTAAGGGTC
1 AAAATGTAA-TTTTTGGAAGTTTGAGGGTC
* *
811 AAAATGTAATTTTTGGAAAGTTCGAGGGTT
1 AAAATGTAATTTTTGG-AAGTTTGAGGGTC
*
841 AAAATGTAATTTTTGAGAAGTTCGAGGGTC
1 AAAATGTAATTTTTG-GAAGTTTGAGGGTC
*
871 AAAATGTATTTTTTGAGAAGTTTGAGGGTC
1 AAAATGTAATTTTTG-GAAGTTTGAGGGTC
* * * *
901 AAAATGCATTTTTTGGAAAGTTCGGGGGTC
1 AAAATGTAATTTTTGG-AAGTTTGAGGGTC
931 AAAA
1 AAAA
935 CATGATTTTT
Statistics
Matches: 153, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
28 11 0.07
29 32 0.21
30 109 0.71
31 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTGAGGGTC
Found at i:869 original size:60 final size:59
Alignment explanation
Indices: 685--934 Score: 217
Period size: 60 Copynumber: 4.2 Consensus size: 59
675 TTTTGGATAC
* ** *
685 TCGAGAGT-AAAATGGTAATTTTTGGAAAGTTCG-GAATAAAAATGGTAATTTTTGGATA-T
1 TCGAGGGTCAAAAT-GTAATTTTTGGAAAGTTCGAGGGTTAAAAT-GTAATTTTTGGA-AGT
* * * * * **
744 TTGAGGGTAAAAATGTGATTTTT-GAAAGTTC-AGGGGTAACATGTAATTTTTTATAAGCT
1 TCGAGGGTCAAAATGTAATTTTTGGAAAGTTCGAGGGTTAAAATGTAA-TTTTTGGAAG-T
*
803 T-AAGGGTCAAAATGTAATTTTTGGAAAGTTCGAGGGTTAAAATGTAATTTTTGAGAAGT
1 TCGAGGGTCAAAATGTAATTTTTGGAAAGTTCGAGGGTTAAAATGTAATTTTTG-GAAGT
* * * * *
862 TCGAGGGTCAAAATGT-ATTTTTTGAGAAGTTTGAGGGTCAAAATGCATTTTTTGGAAAGT
1 TCGAGGGTCAAAATGTAATTTTTGGA-AAGTTCGAGGGTTAAAATGTAATTTTTGG-AAGT
*
922 TCGGGGGTCAAAA
1 TCGAGGGTCAAAA
935 CATGATTTTT
Statistics
Matches: 156, Mismatches: 24, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
57 5 0.03
58 37 0.24
59 40 0.26
60 74 0.47
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.36
Consensus pattern (59 bp):
TCGAGGGTCAAAATGTAATTTTTGGAAAGTTCGAGGGTTAAAATGTAATTTTTGGAAGT
Found at i:914 original size:90 final size:88
Alignment explanation
Indices: 731--934 Score: 243
Period size: 90 Copynumber: 2.3 Consensus size: 88
721 TAAAAATGGT
* * * *
731 AATTTTTGGATA-TTTGAGGGTAAAAATGTGATTTTTGAAAGTTCAGGGGTAACATGTAATTTTT
1 AATTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTCAGGGGTAAAATGTAATTTTT
* *
795 TATAAGCTTAAGGGTCAAAATGT
66 TAGAAGCTTAAGGGTCAAAATGC
*
818 AATTTTTGGAAAGTTCGAGGGTTAAAATGTAATTTTTGAGAAGTTC-GAGGGTCAAAATGT-ATT
1 AATTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGA-AAGTTCAG-GGGT-AAAATGTAATT
* *
881 TTTTGAGAAGTTTGAGGGTCAAAATGC
63 TTTT-AGAAGCTTAAGGGTCAAAATGC
* * *
908 ATTTTTTGGAAAGTTCGGGGGTCAAAA
1 AATTTTTGGAAAGTTCGAGGGTAAAAA
935 CATGATTTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
87 11 0.11
88 24 0.24
89 17 0.17
90 48 0.48
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.37
Consensus pattern (88 bp):
AATTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTCAGGGGTAAAATGTAATTTTT
TAGAAGCTTAAGGGTCAAAATGC
Done.